Instructions for Using TreeView
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Introduction
Michael Eisen developed the TreeView program when he was at Stanford University. The purpose of this program is to “Graphically browse results of clustering and other analyses from Cluster.” In addition to visualizing the microarray data, we use TreeView to generate figures for publication. The TreeView algorithm is available for Windows, MAC, Linux, and Unix. For more information, check out:
- http://rana.lbl.gov/EisenSoftware.htm (Eisen’s homepage includes the manual, software, and links to other sites)
- ClusterTreeView.pdf (Manual for Cluster and TreeView)
Using TreeView to Display a Node-Map
Select File, Load, and pick the *.cdt file that one wants an image of
Select Setting, Options to bring up the OptionsForm dialog.
The Display tab has options for adjusting the pixel size of each image, thumbnail and zoom, and the Image Contrast. We don’t Mask Values.
TreeView uses the numerical values to assign a color scale to the data. The contrast setting allows one to determine the amount of contrast between the smallest and largest value. The lower the contrast setting, the less gradation exists between the two extremes (see image panel to right
Notice how as one decreases the contrast, the spots look brighter, but we lose the intermediate values and our ability to see shades in between.
Note that it’s important to remember the contrast setting and use the same setting for the color scale (see Howto Create a Color Scale)
Select the Colors tab.
Select the color box (Negative, Zero, Positive, or Missing) to pick a color for that particular value. The default color scale is a red-green scale. It’s a good idea to use a different color scale, such as yellow-blue, for people who may be color blind. Remember that the data is in log scale so for the yellow-blue scale, yellow represents the positive values (high antigen-antibody reactivity), black represents zero (intermediate antigen-antibody reactivity), and blue represents negative values (low or no antigen-antibody reactivity). One can also Save or Load color schemes that are frequently used.
Make sure to select Apply when finished.
Selecting the Nodes
Select the farthest node to the left in the thumbnail image to view the entire image. All the nodes will become highlighted and a zoom image should appear. If there are many samples, the zoom image may not show them all initially. Move the cursor near the right edge of the Zoom Image and opposite pointing arrows should appear. When the arrows appear, press the left mouse button and drag the panel to increase the viewing area. Select the farthest node on the thumbnail image again to refresh the display.
Saving the Image
Select File, Save PS Image
Make sure every option has a check next to its name.
Gene Tree (nodes for the sample names)
Gene Labels (names of the samples)
Picture (color display of the data)
Array Tree (nodes for the antigen names)
Array Labels (names of the antigens)
Choose the block size (pixel size for the output) for the image. An 8 x 8 image is an excellent choice for images. One may go larger or smaller depending on size constraints for publishing.
Select Save and name the file.
Congratulations, you’ve made a Node-Map!
Using TreeView to Display a Heatmap
Launch the TreeView program – version 1.60
Select File, Load, and pick the *.cdt file that one wants an image of
Select Setting, Options to bring up the OptionsForm dialog.
For a heatmap, one must adjust the thumbnail image size so that the entire image fits in the window (a 1 x 1 image setting is typical for the entire proteome). The contrast and color setting are the same as with a Node-Map (see above).
Make sure to select Apply when finished.
Selecting the Entire Map
Move the mouse cursor to the upper left corner of the thumbnail image. Press the left mouse button and drag the yellow frame around the entire map. Release the left mouse button and the zoom image should show the entire map. It's a good idea to double check the first and the last antigen name to make sure that you successfully highlighted the entire map. A scroll bar should appear next to the antigen names to scroll up/down for viewing the entire map. If the first try wasn’t successful, then simply try again.
Note also that one will have to highlight the entire map again after any changes to the settings.
Saving the Image
Select File, Save PS Image
For a heatmap, even though every option may be checked, other the picture and labels will show up.
Choose the block size (pixel size for the output) for the image. An 8 x 8 image is an excellent choice for image; however, one may go smaller for a heatmap.
Select Save and name the file.
Congratulations, you’ve made a Heatmap!
[1] The version is not important. Version 1.60 is simply the most recent version and the one I will refer to in this document.
rian A. Kidd Ó 2004